Understanding pneumococcal serotype 1 biology through population genomic analysis

Area of Science:

• Genomics
• Epidemiology
• Microbiology

Background:

• Streptococcus pneumoniae causes over one million child deaths annually, disproportionately affecting low-income countries.
• The ST217 clone of serotype 1 pneumococci is a major contributor to the disease burden in Sub-Saharan Africa.
• HIV infection exacerbates pneumococcal disease severity in Sub-Saharan Africa.

Purpose of the Study:

• To investigate the evolutionary history and population structure of the globally distributed ST217 pneumococcus clone.
• To identify factors contributing to the virulence and geographic adaptation of the ST217 clone.
• To assess the prevalence of antibiotic resistance genes within the ST217 lineage.

Main Methods:

• Whole genome sequencing of 226 ST217 isolates from African and Asian countries.
• Phylogenetic and coalescent analyses to infer evolutionary relationships and population dynamics.
• Screening of genomes for antibiotic resistance genes and mobile genetic elements.

Main Results:

• The ST217 clone exhibits high phylogeographic diversity, with distinct clusters associated with specific regions, indicating long-term global circulation and adaptation.
• Lower than expected genomic sequence diversity suggests strong purifying selection and population bottlenecks.
• African isolates displayed a higher prevalence of antibiotic resistance genes compared to Asian isolates, with specific deletions in resistance elements observed in West African strains.

Conclusions:

• The ST217 clone's long history of global circulation has facilitated its diversification and adaptation to diverse geographical regions and selection pressures.
• The clone's invasive nature contrasts with its limited ability for long-term nasopharyngeal colonization, potentially explaining its lower recombination rates.
• Further research is needed to elucidate the biological mechanisms underlying the ST217 clone's invasiveness and colonization dynamics.